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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.19

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-01-09, 15:10 CET based on data in: /auto/brno2/home/kratka/outbreak_metagenomic_sim/results/fastqc


        General Statistics

        Showing 172/172 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        HTP_01_03_2021_INF_unenriched_1
        72.8%
        47%
        101 bp
        9.6
        HTP_01_03_2021_INF_unenriched_2
        73.3%
        47%
        101 bp
        9.6
        HTP_10_02_2020_INF_unenriched_1
        33.3%
        55%
        151 bp
        4.6
        HTP_10_02_2020_INF_unenriched_2
        15.6%
        56%
        151 bp
        4.6
        HTP_10_13_2020_INF_unenriched_1
        37.9%
        55%
        151 bp
        2.2
        HTP_10_13_2020_INF_unenriched_2
        22.4%
        55%
        151 bp
        2.2
        HTP_10_20_2020_INF_unenriched_1
        28.4%
        57%
        151 bp
        4.4
        HTP_10_20_2020_INF_unenriched_2
        13.8%
        56%
        151 bp
        4.4
        HTP_10_27_2020_INF_unenriched_1
        46.0%
        54%
        151 bp
        4.2
        HTP_10_27_2020_INF_unenriched_2
        26.4%
        52%
        151 bp
        4.2
        HTP_11_17_2020_INF_unenriched_1
        77.0%
        47%
        101 bp
        16.4
        HTP_11_17_2020_INF_unenriched_2
        76.8%
        48%
        101 bp
        16.4
        HTP_11_24_2020_INF_unenriched_1
        73.4%
        49%
        101 bp
        11.0
        HTP_11_24_2020_INF_unenriched_2
        73.3%
        48%
        101 bp
        11.0
        HTP_11_3_2020_INF_unenriched_1
        73.9%
        49%
        101 bp
        11.5
        HTP_11_3_2020_INF_unenriched_2
        73.7%
        48%
        101 bp
        11.5
        HTP_12_01_2020_INF_unenriched_1
        75.2%
        47%
        101 bp
        11.9
        HTP_12_01_2020_INF_unenriched_2
        74.9%
        48%
        101 bp
        11.9
        HTP_12_04_2020_INF_unenriched_1
        73.7%
        50%
        101 bp
        10.9
        HTP_12_04_2020_INF_unenriched_2
        73.6%
        50%
        101 bp
        10.9
        HTP_12_15_2020_INF_unenriched_1
        75.5%
        49%
        101 bp
        12.0
        HTP_12_15_2020_INF_unenriched_2
        75.4%
        49%
        101 bp
        12.0
        HTP_12_22_2020_INF_unenriched_1
        69.1%
        50%
        101 bp
        8.9
        HTP_12_22_2020_INF_unenriched_2
        69.3%
        50%
        101 bp
        8.9
        HTP_12_29_2020_INF_unenriched_1
        69.3%
        49%
        101 bp
        11.5
        HTP_12_29_2020_INF_unenriched_2
        74.0%
        49%
        101 bp
        11.5
        HTP_1_10_21_1
        42.6%
        50%
        101 bp
        16.1
        HTP_1_12_21_1
        70.1%
        51%
        101 bp
        19.4
        HTP_1_12_21_2
        70.6%
        51%
        101 bp
        19.4
        HTP_1_14_21_1
        21.2%
        50%
        101 bp
        35.5
        HTP_1_14_21_2
        20.5%
        51%
        101 bp
        35.5
        HTP_1_19_21_1
        16.9%
        41%
        101 bp
        42.1
        HTP_1_19_21_2
        16.7%
        41%
        101 bp
        42.1
        HTP_1_21_21_1
        26.7%
        51%
        101 bp
        33.1
        HTP_1_21_21_2
        26.4%
        50%
        101 bp
        33.1
        HTP_1_24_21_1
        52.6%
        44%
        101 bp
        14.5
        HTP_1_24_21_2
        52.9%
        44%
        101 bp
        14.5
        HTP_1_26_21_1
        78.8%
        49%
        101 bp
        14.7
        HTP_1_26_21_2
        76.6%
        50%
        101 bp
        14.7
        HTP_1_28_21_1
        5.6%
        46%
        101 bp
        8.6
        HTP_1_28_21_2
        5.4%
        46%
        101 bp
        8.6
        HTP_1_31_21_1
        37.4%
        50%
        101 bp
        31.2
        HTP_1_31_21_2
        37.4%
        49%
        101 bp
        31.2
        HTP_1_5_21_1
        31.0%
        51%
        101 bp
        30.2
        HTP_1_7_21_1
        20.8%
        51%
        101 bp
        30.1
        HTP_1_7_21_2
        20.5%
        51%
        101 bp
        30.1
        HTP_2_10_21_1
        75.1%
        52%
        101 bp
        24.3
        HTP_2_10_21_2
        76.2%
        52%
        101 bp
        24.3
        HTP_2_15_21_1
        73.6%
        50%
        101 bp
        20.6
        HTP_2_15_21_2
        73.1%
        50%
        101 bp
        20.6
        HTP_2_16_21_1
        40.3%
        50%
        101 bp
        21.8
        HTP_2_16_21_2
        40.2%
        49%
        101 bp
        21.8
        HTP_2_18_21_1
        21.1%
        50%
        101 bp
        42.2
        HTP_2_18_21_2
        20.6%
        50%
        101 bp
        42.2
        HTP_2_21_21_1
        76.5%
        52%
        101 bp
        15.3
        HTP_2_21_21_2
        77.7%
        51%
        101 bp
        15.3
        HTP_2_28_21_1
        67.7%
        50%
        101 bp
        19.4
        HTP_2_2_21_1
        44.3%
        51%
        101 bp
        22.1
        HTP_2_2_21_2
        44.0%
        51%
        101 bp
        22.1
        HTP_2_7_21_1
        66.7%
        51%
        101 bp
        26.5
        HTP_2_7_21_2
        67.0%
        52%
        101 bp
        26.5
        HTP_2_9_21_1
        75.2%
        52%
        101 bp
        28.9
        HTP_2_9_21_2
        74.5%
        52%
        101 bp
        28.9
        HTP_3_11_21_1
        39.4%
        52%
        101 bp
        88.9
        HTP_3_11_21_2
        38.4%
        52%
        101 bp
        88.9
        HTP_3_14_21_1
        37.5%
        51%
        101 bp
        23.3
        HTP_3_14_21_2
        42.2%
        51%
        101 bp
        54.1
        HTP_3_18_2021_1
        34.7%
        48%
        101 bp
        28.4
        HTP_3_18_2021_2
        34.3%
        47%
        101 bp
        28.4
        HTP_3_21_2021_1
        60.0%
        46%
        101 bp
        21.0
        HTP_3_21_2021_2
        57.5%
        48%
        101 bp
        21.0
        HTP_3_23_2021_1
        86.9%
        51%
        101 bp
        24.1
        HTP_3_23_2021_2
        85.7%
        52%
        101 bp
        24.1
        HTP_3_25_2021_1
        88.6%
        59%
        101 bp
        17.3
        HTP_3_25_2021_2
        87.9%
        63%
        101 bp
        17.3
        HTP_3_29_2021_1
        35.2%
        47%
        101 bp
        19.2
        HTP_3_29_2021_2
        35.0%
        47%
        101 bp
        19.2
        HTP_3_2_21_1
        64.9%
        51%
        101 bp
        15.9
        HTP_3_2_21_2
        64.3%
        50%
        101 bp
        15.9
        HTP_3_30_2021_1
        58.5%
        48%
        101 bp
        25.3
        HTP_3_30_2021_2
        58.3%
        48%
        101 bp
        25.3
        HTP_3_31_2021_1
        65.8%
        52%
        101 bp
        20.1
        HTP_3_31_2021_2
        65.1%
        54%
        101 bp
        20.1
        HTP_3_4_21_1
        34.8%
        51%
        101 bp
        81.5
        HTP_3_4_21_2
        34.0%
        51%
        101 bp
        81.5
        HTP_3_7_21_1
        42.2%
        51%
        101 bp
        46.0
        HTP_3_7_21_2
        41.7%
        51%
        101 bp
        46.0
        HTP_3_9_21_1
        54.0%
        51%
        101 bp
        33.0
        HTP_3_9_21_2
        56.5%
        52%
        101 bp
        33.0
        HTP_4_15_2021_1
        46.3%
        48%
        101 bp
        16.2
        HTP_4_15_2021_2
        44.5%
        49%
        101 bp
        16.2
        HTP_4_22_2021_1
        21.5%
        50%
        101 bp
        22.5
        HTP_4_22_2021_2
        21.4%
        50%
        101 bp
        22.5
        HTP_4_25_2021_1
        72.3%
        51%
        101 bp
        24.2
        HTP_4_25_2021_2
        72.3%
        50%
        101 bp
        24.2
        HTP_4_26_2021_1
        21.2%
        51%
        101 bp
        26.7
        HTP_4_26_2021_2
        20.9%
        51%
        101 bp
        26.7
        HTP_4_29_2021_1
        15.3%
        52%
        101 bp
        14.9
        HTP_4_29_2021_2
        15.6%
        52%
        101 bp
        18.1
        HTP_4_4_2021_1
        15.8%
        39%
        101 bp
        33.5
        HTP_4_4_2021_2
        15.4%
        39%
        101 bp
        33.5
        HTP_4_6_2021_1
        21.4%
        42%
        101 bp
        33.3
        HTP_4_6_2021_2
        21.3%
        42%
        101 bp
        33.3
        HTP_4_8_2021_1
        20.3%
        38%
        101 bp
        26.3
        HTP_4_8_2021_2
        19.6%
        39%
        101 bp
        26.3
        HTP_5_11_2021_1
        58.3%
        49%
        101 bp
        18.5
        HTP_5_11_2021_2
        58.3%
        50%
        101 bp
        18.5
        HTP_5_13_2021_1
        77.6%
        51%
        101 bp
        19.1
        HTP_5_13_2021_2
        77.5%
        51%
        101 bp
        19.1
        HTP_5_16_2021_1
        15.9%
        49%
        101 bp
        63.1
        HTP_5_16_2021_2
        15.5%
        49%
        101 bp
        63.1
        HTP_5_18_2021_1
        13.0%
        49%
        101 bp
        60.5
        HTP_5_18_2021_2
        12.2%
        49%
        101 bp
        60.5
        HTP_5_20_2021_1
        12.5%
        49%
        101 bp
        54.1
        HTP_5_20_2021_2
        12.4%
        49%
        101 bp
        54.1
        HTP_5_23_2021_1
        18.6%
        48%
        101 bp
        53.3
        HTP_5_24_2021_1
        19.7%
        41%
        101 bp
        32.5
        HTP_5_24_2021_2
        19.3%
        41%
        101 bp
        32.5
        HTP_5_25_2021_1
        18.7%
        41%
        101 bp
        41.6
        HTP_5_25_2021_2
        17.2%
        42%
        101 bp
        41.6
        HTP_5_31_2021_1
        17.7%
        42%
        101 bp
        45.6
        HTP_5_31_2021_2
        16.7%
        42%
        101 bp
        45.6
        HTP_5_4_2021_1
        26.6%
        53%
        101 bp
        21.0
        HTP_5_4_2021_2
        26.3%
        54%
        101 bp
        21.0
        HTP_5_6_2021_1
        67.9%
        52%
        101 bp
        18.0
        HTP_5_6_2021_2
        67.8%
        52%
        101 bp
        18.0
        HTP_5_9_2021_1
        64.3%
        53%
        101 bp
        19.2
        HTP_5_9_2021_2
        63.6%
        54%
        101 bp
        19.2
        HTP_6_10_2021_1
        24.5%
        51%
        101 bp
        35.4
        HTP_6_10_2021_2
        24.3%
        51%
        101 bp
        35.4
        HTP_6_15_2021_1
        24.8%
        50%
        101 bp
        28.6
        HTP_6_15_2021_2
        24.3%
        50%
        101 bp
        28.6
        HTP_6_1_2021_1
        15.6%
        46%
        101 bp
        54.0
        HTP_6_1_2021_2
        13.7%
        46%
        101 bp
        54.0
        HTP_6_20_2021_1
        66.6%
        50%
        101 bp
        28.3
        HTP_6_20_2021_2
        65.2%
        50%
        101 bp
        28.3
        HTP_6_24_2021_1
        43.6%
        50%
        101 bp
        33.7
        HTP_6_24_2021_2
        42.6%
        51%
        101 bp
        33.7
        HTP_6_27_2021_1
        32.6%
        50%
        101 bp
        45.7
        HTP_6_27_2021_2
        32.2%
        50%
        101 bp
        45.7
        HTP_6_3_2021_1
        21.3%
        49%
        101 bp
        31.2
        HTP_6_3_2021_2
        20.6%
        49%
        101 bp
        31.2
        HTP_6_6_2021_1
        21.5%
        48%
        101 bp
        50.7
        HTP_6_6_2021_2
        21.2%
        48%
        101 bp
        50.7
        HTP_7_13_2021_1
        68.9%
        50%
        101 bp
        29.6
        HTP_7_13_2021_2
        68.0%
        51%
        101 bp
        29.6
        HTP_7_15_2021_1
        25.0%
        50%
        101 bp
        36.1
        HTP_7_15_2021_2
        24.5%
        50%
        101 bp
        36.1
        HTP_7_1_2021_1
        31.2%
        51%
        101 bp
        43.2
        HTP_7_1_2021_2
        30.7%
        51%
        101 bp
        43.2
        HTP_7_22_2021_1
        66.6%
        50%
        101 bp
        33.0
        HTP_7_22_2021_2
        65.8%
        50%
        101 bp
        33.0
        HTP_7_29_2021_1
        37.7%
        49%
        101 bp
        43.9
        HTP_7_29_2021_2
        37.4%
        49%
        101 bp
        43.9
        HTP_7_8_2021_1
        53.0%
        49%
        101 bp
        26.9
        HTP_7_8_2021_2
        52.1%
        50%
        101 bp
        26.9
        HTP_8_11_2020_INF_unenriched_1
        49.0%
        53%
        151 bp
        3.3
        HTP_8_11_2020_INF_unenriched_2
        29.0%
        55%
        151 bp
        3.3
        HTP_8_18_2020_INF_unenriched_1
        45.3%
        55%
        151 bp
        2.8
        HTP_8_18_2020_INF_unenriched_2
        21.9%
        55%
        151 bp
        2.8
        HTP_8_25_2020_INF_unenriched_1
        28.9%
        55%
        151 bp
        3.5
        HTP_8_25_2020_INF_unenriched_2
        12.2%
        54%
        151 bp
        3.5
        HTP_9_01_2020_INF_unenriched_1
        39.4%
        54%
        151 bp
        3.6
        HTP_9_01_2020_INF_unenriched_2
        21.1%
        55%
        151 bp
        3.6
        HTP_9_08_2020_INF_unenriched_1
        30.4%
        54%
        151 bp
        3.6
        HTP_9_08_2020_INF_unenriched_2
        12.7%
        53%
        151 bp
        3.6
        HTP_9_15_2020_INF_unenriched_1
        45.4%
        52%
        151 bp
        3.6
        HTP_9_15_2020_INF_unenriched_2
        25.0%
        54%
        151 bp
        3.6
        HTP_9_22_2020_INF_unenriched_1
        77.3%
        48%
        101 bp
        12.9
        HTP_9_22_2020_INF_unenriched_2
        77.2%
        47%
        101 bp
        12.9
        HTP_9_29_2020_INF_unenriched_1
        80.8%
        49%
        101 bp
        13.6
        HTP_9_29_2020_INF_unenriched_2
        80.6%
        49%
        101 bp
        13.6

        FastQC

        Versions: 0.11.9, 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
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        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (101bp , 151bp). See the General Statistics Table.

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        34
        6914794
        0.1551%
        CCTTATAGCCACCGTTGCGTCATCTACTCTACGAGTAGCGTCTAACGTTT
        16
        268856
        0.0060%
        GTACAGGCATATGATTAAAGCGCAACCTAAGCAGAAGCTGGATACATCAA
        11
        160460
        0.0036%
        CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
        2
        117704
        0.0026%
        GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG
        2
        105904
        0.0024%
        GCGCATGGCAGGCAGTTTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGG
        2
        47410
        0.0011%
        GGCTCAGACCGGTCGGAAATCGGTCGTTGAGTGCAATGGCATAAGCCTGC
        2
        44421
        0.0010%
        GTCTCACGACGTTCTGAACCCAGCTCACGTACCACTTTAATCGGCGAACA
        2
        43470
        0.0010%
        GAGGAAAGGACATCAACGAGACTCCGTCAGTAGTGGCGAGCGAACGCGGA
        2
        37302
        0.0008%
        GGCCAGTGCCTGTGTGGAGTTTACCGGAACGGTCTGGAATGGCCGGCGAG
        2
        36534
        0.0008%
        AGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCAGACCA
        2
        37346
        0.0008%
        CTCTACTTGTGCGCTATCGGTCTCCGGCCAATATTTAGCTTTAGATGAAA
        2
        211841
        0.0048%
        GTTCTAAGTTGGTCGTTAATCGCCCGCCGGACGGCCGAAGCCTGCCAAGG
        2
        136434
        0.0031%
        GGCATGCCCTCCGGAATACCAGAGGGCGCAATGTGCGTTCAAAGACTCGA
        2
        104425
        0.0023%
        ATCTATCCCCGCGCGAGGTGACATTACAATCCGCCAGCCAGCTCCCAGGG
        2
        100158
        0.0022%
        ATTTAGAGCTGCATTCCCAAACAACTCGACTCGTCGAAGGAGCTTCACAC
        2
        85278
        0.0019%
        GCGCAAGGCCATGCGATTCGTTAAGTTATTATGATTCACCAAGGAGCCCC
        2
        82434
        0.0018%
        GTCCCCATCTAAGTGCCCTGGAACGGGACGTCATAGAGGGTGAGAATCCC
        2
        76340
        0.0017%
        GTGCCGAACGGGTCATTATAGAATCCCGTCCGATCCCTAGTCGGCATAGT
        2
        77713
        0.0017%
        CTCTATGACGTCCCGTTCCAGGGCACTTAGATGGGGACCGCTCCCGAAGC
        2
        72636
        0.0016%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.11.9, 0.12.1